BN0635 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 2 1.9792e-05 8.2756e-03
Layer 3 4.3259e-05 5.0583e-03
Layer 5 1.9385e-04 1.6971e-03
Layer 4 2.7582e-04 1.1086e-03
Layer 6 8.7535e-04 9.3490e-03
Layer 1 2.3428e-02 1.2027e-01
WM 8.0865e-01 4.2027e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
NRGN Expression Distribution
Gene Specificity Score (GSS)
NRGN GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
NRGN Layer 2 2.6426 0.6592
SNCA Layer 4 2.0586 0.6566
HSP90AB1 Layer 2 2.3711 0.6500
CAMK2B Layer 2 2.4639 0.6366
SLC17A7 Layer 2 2.3340 0.6314
BASP1 Layer 4 2.5215 0.6281
GPM6A Layer 2 2.2227 0.6186
TUBA1B Layer 3 2.3809 0.6161
YWHAB Layer 2 2.4727 0.6116
LMO4 Layer 4 2.2744 0.6043
CELF2 Layer 5 2.2363 0.6043
CHN1 Layer 2 2.3867 0.6020
VAMP2 Layer 3 2.3125 0.6018
SNAP25 Layer 2 2.4668 0.6008
PPP2R1A Layer 2 2.2070 0.6005
DNM1 Layer 5 2.2129 0.5931
FTL Layer 2 2.3242 0.5928
MAP2 Layer 2 2.3398 0.5902
FAIM2 Layer 2 2.4238 0.5893
GRIN1 Layer 4 2.6133 0.5880
FTH1 Layer 2 2.0586 0.5871
MAP1A Layer 3 2.3555 0.5870
ATP6V0C Layer 2 2.3994 0.5869
SYT1 Layer 5 2.3867 0.5855
MAP1B Layer 3 2.2031 0.5843
MEF2C Layer 4 2.5449 0.5827
PRKAR1B Layer 4 2.3340 0.5818
ARPP19 Layer 2 2.5508 0.5812
MT3 Layer 1 2.0723 0.5798
NECAB1 Layer 3 2.2324 0.5798
IDS Layer 2 2.4180 0.5778
ELAVL3 Layer 2 2.4453 0.5760
ENO2 Layer 4 2.2031 0.5739
JUND Layer 5 2.3340 0.5739
ZBTB7A Layer 3 2.4082 0.5724
GLUL Layer 2 2.2715 0.5719
CLU Layer 1 2.2422 0.5706
HSP90AA1 Layer 2 1.9990 0.5689
THY1 Layer 2 2.2422 0.5688
EEF1A2 Layer 5 2.1543 0.5650
MEG3 Layer 2 2.2998 0.5647
PTMS Layer 2 2.4941 0.5647
C5orf63 Layer 5 2.2930 0.5636
RAC1 Layer 2 2.2744 0.5636
RTN3 Layer 2 2.3398 0.5635
NORAD Layer 4 2.1699 0.5628
CALM1 Layer 2 2.5605 0.5616
TCF4 Layer 4 2.2773 0.5614
ARL6IP1 Layer 3 2.2676 0.5612
NEFL Layer 3 2.5781 0.5605

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN0635
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN0635_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0635/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0635/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0635/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0635/report/PD/BN0635_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0635/report/PD/BN0635_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 00:48:31
  • Number of Processes: 10
  • Spending Time: 0h 3m